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For: Sherlock ME, Sudarsan N, Stav S, Breaker RR. Tandem riboswitches form a natural Boolean logic gate to control purine metabolism in bacteria. eLife 2018;7:e33908. [PMID: 29504937 PMCID: PMC5912903 DOI: 10.7554/elife.33908] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 03/04/2018] [Indexed: 12/28/2022]  Open
Number Cited by Other Article(s)
1
Lin X, Huang Y, Huang J, Yuan H, Luo Y, Lu Z, Ao Y, Huang J, Chen SB, Miao Z, Huang L. From Theophylline to Adenine or preQ1: Repurposing a DNA Aptamer Revealed by Crystal Structure Analysis. Angew Chem Int Ed Engl 2025;64:e202504107. [PMID: 40101171 DOI: 10.1002/anie.202504107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2025] [Revised: 03/13/2025] [Accepted: 03/18/2025] [Indexed: 03/20/2025]
2
Xiao W, Liu G, Chen T, Zhang Y, Ke A, Cai R, Lu C. Escherichia coli yybP-ykoY Riboswitch as a Tandem Riboswitch Regulated by Mn2+ and pH. ACS Chem Biol 2025;20:1010-1019. [PMID: 40252020 DOI: 10.1021/acschembio.4c00715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/21/2025]
3
Barth KM, Hiller DA, Belem de Andrade G, Kavita K, Fernando CM, Breaker RR, Strobel SA. Decoding the Complex Functional Landscape of the ykkC Riboswitches. Biochemistry 2025;64:1983-1995. [PMID: 40254862 DOI: 10.1021/acs.biochem.4c00787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/22/2025]
4
Kelvin D, Arias Rodriguez J, Groher AC, Petras K, Suess B. Synthetic Dual-Input Hybrid Riboswitches─Optimized Genetic Regulators in Yeast. ACS Synth Biol 2025;14:497-509. [PMID: 39902969 PMCID: PMC11854369 DOI: 10.1021/acssynbio.4c00660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2024] [Revised: 01/15/2025] [Accepted: 01/22/2025] [Indexed: 02/06/2025]
5
Capdevila DA, Rondón JJ, Edmonds KA, Rocchio JS, Dujovne MV, Giedroc DP. Bacterial Metallostasis: Metal Sensing, Metalloproteome Remodeling, and Metal Trafficking. Chem Rev 2024;124:13574-13659. [PMID: 39658019 DOI: 10.1021/acs.chemrev.4c00264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2024]
6
Feng S, Xiao W, Yu Y, Liu G, Zhang Y, Chen T, Lu C. Linker-Mediated Inactivation of the SAM-II Domain in the Tandem SAM-II/SAM-V Riboswitch. Int J Mol Sci 2024;25:11288. [PMID: 39457069 PMCID: PMC11508383 DOI: 10.3390/ijms252011288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2024] [Revised: 10/16/2024] [Accepted: 10/18/2024] [Indexed: 10/28/2024]  Open
7
Barth KM, Hiller DA, Strobel SA. The Impact of Second-Shell Nucleotides on Ligand Specificity in Cyclic Dinucleotide Riboswitches. Biochemistry 2024:10.1021/acs.biochem.3c00586. [PMID: 38329042 PMCID: PMC11306416 DOI: 10.1021/acs.biochem.3c00586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
8
Wu Y, Zhu L, Zhang Y, Xu W. Multidimensional Applications and Challenges of Riboswitches in Biosensing and Biotherapy. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024;20:e2304852. [PMID: 37658499 DOI: 10.1002/smll.202304852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 08/15/2023] [Indexed: 09/03/2023]
9
Salvail H, Balaji A, Roth A, Breaker RR. A spermidine riboswitch class in bacteria exploits a close variant of an aptamer for the enzyme cofactor S-adenosylmethionine. Cell Rep 2023;42:113571. [PMID: 38096053 PMCID: PMC10853860 DOI: 10.1016/j.celrep.2023.113571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 10/16/2023] [Accepted: 11/22/2023] [Indexed: 12/30/2023]  Open
10
Szyjka CE, Strobel EJ. Observation of coordinated RNA folding events by systematic cotranscriptional RNA structure probing. Nat Commun 2023;14:7839. [PMID: 38030633 PMCID: PMC10687018 DOI: 10.1038/s41467-023-43395-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 11/08/2023] [Indexed: 12/01/2023]  Open
11
Hamal Dhakal S, Kavita K, Panchapakesan SSS, Roth A, Breaker RR. 8-oxoguanine riboswitches in bacteria detect and respond to oxidative DNA damage. Proc Natl Acad Sci U S A 2023;120:e2307854120. [PMID: 37748066 PMCID: PMC10556655 DOI: 10.1073/pnas.2307854120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 08/25/2023] [Indexed: 09/27/2023]  Open
12
Xu J, Hou J, Ding M, Wang Z, Chen T. Riboswitches, from cognition to transformation. Synth Syst Biotechnol 2023;8:357-370. [PMID: 37325181 PMCID: PMC10265488 DOI: 10.1016/j.synbio.2023.05.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 05/20/2023] [Accepted: 05/25/2023] [Indexed: 06/17/2023]  Open
13
Ferreira SS, Anderson CE, Antunes MS. A logical way to reprogram plants. Biochem Biophys Res Commun 2023;654:80-86. [PMID: 36898227 DOI: 10.1016/j.bbrc.2023.02.080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 02/27/2023] [Indexed: 03/06/2023]
14
Ortega AD. Real-Time Assessment of Intracellular Metabolites in Single Cells through RNA-Based Sensors. Biomolecules 2023;13:biom13050765. [PMID: 37238635 DOI: 10.3390/biom13050765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 04/24/2023] [Accepted: 04/26/2023] [Indexed: 05/28/2023]  Open
15
Peng X, Liao W, Lin X, Lilley DMJ, Huang L. Crystal structures of the NAD+-II riboswitch reveal two distinct ligand-binding pockets. Nucleic Acids Res 2023;51:2904-2914. [PMID: 36840714 PMCID: PMC10085692 DOI: 10.1093/nar/gkad102] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 02/01/2023] [Accepted: 02/16/2023] [Indexed: 02/26/2023]  Open
16
Szyjka CE, Strobel EJ. Observation of coordinated cotranscriptional RNA folding events. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.21.529405. [PMID: 36865203 PMCID: PMC9980086 DOI: 10.1101/2023.02.21.529405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
17
Kavita K, Breaker RR. Discovering riboswitches: the past and the future. Trends Biochem Sci 2023;48:119-141. [PMID: 36150954 PMCID: PMC10043782 DOI: 10.1016/j.tibs.2022.08.009] [Citation(s) in RCA: 119] [Impact Index Per Article: 59.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 08/18/2022] [Accepted: 08/26/2022] [Indexed: 01/25/2023]
18
Jagodnik J, Tjaden B, Ross W, Gourse R. Identification and characterization of RNA binding sites for (p)ppGpp using RNA-DRaCALA. Nucleic Acids Res 2023;51:852-869. [PMID: 36617997 PMCID: PMC9881157 DOI: 10.1093/nar/gkac1224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 11/30/2022] [Accepted: 01/04/2023] [Indexed: 01/10/2023]  Open
19
Lenkeit F, Eckert I, Sinn M, Hauth F, Hartig JS, Weinberg Z. A variant of guanidine-IV riboswitches exhibits evidence of a distinct ligand specificity. RNA Biol 2023;20:10-19. [PMID: 36548032 PMCID: PMC9788692 DOI: 10.1080/15476286.2022.2160562] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]  Open
20
White N, Sadeeshkumar H, Sun A, Sudarsan N, Breaker RR. Lithium-sensing riboswitch classes regulate expression of bacterial cation transporter genes. Sci Rep 2022;12:19145. [PMID: 36352003 PMCID: PMC9646797 DOI: 10.1038/s41598-022-20695-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 09/16/2022] [Indexed: 11/10/2022]  Open
21
Vikram, Mishra V, Rana A, Ahire JJ. Riboswitch-mediated regulation of riboflavin biosynthesis genes in prokaryotes. 3 Biotech 2022;12:278. [PMID: 36275359 PMCID: PMC9474784 DOI: 10.1007/s13205-022-03348-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 09/02/2022] [Indexed: 11/01/2022]  Open
22
White N, Sadeeshkumar H, Sun A, Sudarsan N, Breaker RR. Na+ riboswitches regulate genes for diverse physiological processes in bacteria. Nat Chem Biol 2022;18:878-885. [PMID: 35879547 PMCID: PMC9337991 DOI: 10.1038/s41589-022-01086-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 06/10/2022] [Indexed: 01/31/2023]
23
Hamal Dhakal S, Panchapakesan SSS, Slattery P, Roth A, Breaker RR. Variants of the guanine riboswitch class exhibit altered ligand specificities for xanthine, guanine, or 2'-deoxyguanosine. Proc Natl Acad Sci U S A 2022;119:e2120246119. [PMID: 35622895 PMCID: PMC9295807 DOI: 10.1073/pnas.2120246119] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 03/12/2022] [Indexed: 12/30/2022]  Open
24
Knappenberger A, Hiller D. How Do Bacteria "See" Molecules Inside Themselves? FRONTIERS FOR YOUNG MINDS 2022;10:686804. [PMID: 36909261 PMCID: PMC9997733 DOI: 10.3389/frym.2022.686804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
25
Breaker RR. The Biochemical Landscape of Riboswitch Ligands. Biochemistry 2022;61:137-149. [PMID: 35068140 PMCID: PMC9971707 DOI: 10.1021/acs.biochem.1c00765] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
26
Chandris P, Giannouli CC, Panayotou G. Imaging Approaches for the Study of Metabolism in Real Time Using Genetically Encoded Reporters. Front Cell Dev Biol 2022;9:725114. [PMID: 35118062 PMCID: PMC8804523 DOI: 10.3389/fcell.2021.725114] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 12/13/2021] [Indexed: 11/23/2022]  Open
27
Sherlock ME, Higgs G, Yu D, Widner DL, White NA, Sudarsan N, Sadeeshkumar H, Perkins KR, Mirihana Arachchilage G, Malkowski SN, King CG, Harris KA, Gaffield G, Atilho RM, Breaker RR. Architectures and complex functions of tandem riboswitches. RNA Biol 2022;19:1059-1076. [PMID: 36093908 PMCID: PMC9481103 DOI: 10.1080/15476286.2022.2119017] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 08/23/2022] [Indexed: 11/16/2022]  Open
28
Scheuer R, Dietz T, Kretz J, Hadjeras L, McIntosh M, Evguenieva-Hackenberg E. Incoherent dual regulation by a SAM-II riboswitch controlling translation at a distance. RNA Biol 2022;19:980-995. [PMID: 35950733 PMCID: PMC9373788 DOI: 10.1080/15476286.2022.2110380] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]  Open
29
Trachman RJ, Ferré-D'Amaré AR. An uncommon [K+(Mg2+)2] metal ion triad imparts stability and selectivity to the Guanidine-I riboswitch. RNA (NEW YORK, N.Y.) 2021;27:1257-1264. [PMID: 34257148 PMCID: PMC8457001 DOI: 10.1261/rna.078824.121] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 07/05/2021] [Indexed: 06/13/2023]
30
Ariza-Mateos A, Nuthanakanti A, Serganov A. Riboswitch Mechanisms: New Tricks for an Old Dog. BIOCHEMISTRY (MOSCOW) 2021;86:962-975. [PMID: 34488573 DOI: 10.1134/s0006297921080071] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
31
Townshend RJL, Eismann S, Watkins AM, Rangan R, Karelina M, Das R, Dror RO. Geometric deep learning of RNA structure. Science 2021;373:1047-1051. [PMID: 34446608 PMCID: PMC9829186 DOI: 10.1126/science.abe5650] [Citation(s) in RCA: 207] [Impact Index Per Article: 51.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 07/14/2021] [Indexed: 01/28/2023]
32
Siblings or doppelgängers? Deciphering the evolution of structured cis-regulatory RNAs beyond homology. Biochem Soc Trans 2021;48:1941-1951. [PMID: 32869842 PMCID: PMC7609027 DOI: 10.1042/bst20191060] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 08/04/2020] [Accepted: 08/06/2020] [Indexed: 11/21/2022]
33
Bange G, Brodersen DE, Liuzzi A, Steinchen W. Two P or Not Two P: Understanding Regulation by the Bacterial Second Messengers (p)ppGpp. Annu Rev Microbiol 2021;75:383-406. [PMID: 34343020 DOI: 10.1146/annurev-micro-042621-122343] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
34
Xu X, Egger M, Chen H, Bartosik K, Micura R, Ren A. Insights into xanthine riboswitch structure and metal ion-mediated ligand recognition. Nucleic Acids Res 2021;49:7139-7153. [PMID: 34125892 PMCID: PMC8266621 DOI: 10.1093/nar/gkab486] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 04/29/2021] [Accepted: 05/27/2021] [Indexed: 12/26/2022]  Open
35
Brewer KI, Greenlee EB, Higgs G, Yu D, Mirihana Arachchilage G, Chen X, King N, White N, Breaker RR. Comprehensive discovery of novel structured noncoding RNAs in 26 bacterial genomes. RNA Biol 2021;18:2417-2432. [PMID: 33970790 PMCID: PMC8632094 DOI: 10.1080/15476286.2021.1917891] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/30/2022]  Open
36
Panchapakesan SSS, Breaker RR. The case of the missing allosteric ribozymes. Nat Chem Biol 2021;17:375-382. [PMID: 33495645 PMCID: PMC8880209 DOI: 10.1038/s41589-020-00713-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 11/13/2020] [Indexed: 01/28/2023]
37
Riboswitch theo/metE as a Transcription Regulation Tool for Xanthomonas citri subsp. citri. Microorganisms 2021;9:microorganisms9020329. [PMID: 33562149 PMCID: PMC7914508 DOI: 10.3390/microorganisms9020329] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 01/30/2021] [Accepted: 02/02/2021] [Indexed: 11/17/2022]  Open
38
Chen H, Egger M, Xu X, Flemmich L, Krasheninina O, Sun A, Micura R, Ren A. Structural distinctions between NAD+ riboswitch domains 1 and 2 determine differential folding and ligand binding. Nucleic Acids Res 2020;48:12394-12406. [PMID: 33170270 PMCID: PMC7708056 DOI: 10.1093/nar/gkaa1029] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 10/12/2020] [Accepted: 10/16/2020] [Indexed: 11/13/2022]  Open
39
Malkowski SN, Atilho RM, Greenlee EB, Weinberg CE, Breaker RR. A rare bacterial RNA motif is implicated in the regulation of the purF gene whose encoded enzyme synthesizes phosphoribosylamine. RNA (NEW YORK, N.Y.) 2020;26:1838-1846. [PMID: 32843366 PMCID: PMC7668255 DOI: 10.1261/rna.077313.120] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 08/14/2020] [Indexed: 05/31/2023]
40
Micura R, Höbartner C. Fundamental studies of functional nucleic acids: aptamers, riboswitches, ribozymes and DNAzymes. Chem Soc Rev 2020;49:7331-7353. [PMID: 32944725 DOI: 10.1039/d0cs00617c] [Citation(s) in RCA: 126] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
41
Breaker RR. Imaginary Ribozymes. ACS Chem Biol 2020;15:2020-2030. [PMID: 32687319 PMCID: PMC7919269 DOI: 10.1021/acschembio.0c00214] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
42
Yu D, Breaker RR. A bacterial riboswitch class senses xanthine and uric acid to regulate genes associated with purine oxidation. RNA (NEW YORK, N.Y.) 2020;26:960-968. [PMID: 32345632 PMCID: PMC7373994 DOI: 10.1261/rna.075218.120] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 04/01/2020] [Indexed: 06/02/2023]
43
Zhang J. Unboxing the T-box riboswitches-A glimpse into multivalent and multimodal RNA-RNA interactions. WILEY INTERDISCIPLINARY REVIEWS-RNA 2020;11:e1600. [PMID: 32633085 PMCID: PMC7583486 DOI: 10.1002/wrna.1600] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 04/25/2020] [Accepted: 04/29/2020] [Indexed: 12/17/2022]
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Sherlock ME, Breaker RR. Former orphan riboswitches reveal unexplored areas of bacterial metabolism, signaling, and gene control processes. RNA (NEW YORK, N.Y.) 2020;26:675-693. [PMID: 32165489 PMCID: PMC7266159 DOI: 10.1261/rna.074997.120] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
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Matyjasik MM, Batey RT. Structural basis for 2'-deoxyguanosine recognition by the 2'-dG-II class of riboswitches. Nucleic Acids Res 2020;47:10931-10941. [PMID: 31598729 PMCID: PMC6847200 DOI: 10.1093/nar/gkz839] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 09/12/2019] [Accepted: 10/05/2019] [Indexed: 12/25/2022]  Open
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Knappenberger AJ, Reiss CW, Focht CM, Strobel SA. A Modular RNA Domain That Confers Differential Ligand Specificity. Biochemistry 2020;59:1361-1366. [PMID: 32202416 DOI: 10.1021/acs.biochem.0c00117] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Malkowski SN, Spencer TCJ, Breaker RR. Evidence that the nadA motif is a bacterial riboswitch for the ubiquitous enzyme cofactor NAD. RNA (NEW YORK, N.Y.) 2019;25:1616-1627. [PMID: 31467147 PMCID: PMC6859854 DOI: 10.1261/rna.072538.119] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 07/29/2019] [Indexed: 05/04/2023]
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Crum M, Ram-Mohan N, Meyer MM. Regulatory context drives conservation of glycine riboswitch aptamers. PLoS Comput Biol 2019;15:e1007564. [PMID: 31860665 PMCID: PMC6944388 DOI: 10.1371/journal.pcbi.1007564] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 01/06/2020] [Accepted: 11/25/2019] [Indexed: 12/13/2022]  Open
49
Pavlova N, Kaloudas D, Penchovsky R. Riboswitch distribution, structure, and function in bacteria. Gene 2019;708:38-48. [PMID: 31128223 DOI: 10.1016/j.gene.2019.05.036] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 05/12/2019] [Accepted: 05/20/2019] [Indexed: 10/26/2022]
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Atilho RM, Mirihana Arachchilage G, Greenlee EB, Knecht KM, Breaker RR. A bacterial riboswitch class for the thiamin precursor HMP-PP employs a terminator-embedded aptamer. eLife 2019;8:45210. [PMID: 30950790 PMCID: PMC6478431 DOI: 10.7554/elife.45210] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 04/04/2019] [Indexed: 12/29/2022]  Open
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